plasmidSPAdes

plasmidSPAdes is a computational tool for the assembly and identification of plasmid sequences from short-read Illumina sequencing data. Developed as an extension of the SPAdes genome assembler, it incorporates a specialized plasmid-aware workflow that constructs assembly graphs enriched with plasmid-specific edge information. The algorithm initiates by performing an initial assembly with SPAdes, then refines this assembly by applying a plasmid reconstruction module. This module detects circular contigs and uses coverage patterns, read-pair connectivity, and k‑mer frequencies to distinguish plasmid-derived sequences from chromosomal fragments. It also incorporates plasmid-specific markers such as replication origin motifs and mobilization genes, improving the precision of plasmid separation.

plasmidSPAdes has been benchmarked against other plasmid assemblers such as plasmidSPAdes (the tool itself), plasmidFinder, and Recycler. Studies report that it achieves higher recall of plasmid sequences while maintaining low false-positive rates, particularly when analyzing complex bacterial metagenomes or mixed strain samples. The method is open-source and distributed under the GPL license, available on GitHub and the SPAdes website. Installation requires Python, BLAST+, and the SPAdes binary, and it supports multithreading, making it suitable for large-scale bacterial genome projects. Users can input raw Illumina reads in FASTQ format, and the tool outputs assembled plasmid contigs in FASTA format along with a detailed assembly report.